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Tuesday, January 27, 2009

Peer review review, or, Creationists? Back of the bus!

The questions should be addressed to the Darwinist community. Why are you so afraid of even listening to the voices of dissent? How can you be so fearful of information? How can you call yourselves scientists?

Time to really address this subject. For the sake of brevity, I will use the terms Darwinist or naturalistic materialistic even though there are those who prefer different terminology or whose philosophy is somewhat different. I know there are NeoDarwinists and Theistic Darwinists and so on and so on so I will acknowledge that at the start and then move on.

Abstract

Despite the centrality of peer review to the development of a scholarly community, very little is known about the biblical basis and Christian conduct of peer review. We find that peer review is rooted in several Christian virtues, such as reflecting Christ, being honest, seeking wisdom, humbly submitting, showing Christian love, correcting error, and being accountable. Given these principles, we recommend that creationists use a double-blind peer review system, wherein the identities of the author and peer reviewers are confidential. Additionally, we recommend that creationist publishers develop a regular public audit of their peer-review process.

Critics of creationism and Intelligent Design (ID) often note that creationist or ID research does not appear in peer-reviewed literature (e.g., Crawford 1982; Scott and Branch 2003; Max 2004; Bottaro et al. 2006). Creationists complain that we are excluded from the peer-reviewed literature (Anderson 2002; Kulikovsky 2008; see also Tipler 2004) and are therefore required to publish in our own peer reviewed-literature (Morris 2003). Critics view creationist peer review as not “real” peer review. For example, recent attempts to launch new creationist peer-reviewed journals have been met with scorn or dismissal (Sparks et al. 2007; Brumfiel 2008).

The irony of this conflict over peer review is that peer review is poorly understood and criticized even in conventional journals. Over the past 25 years, the process of peer review has come under increasing scrutiny, especially in the biomedical community (e.g., Lock 1986; Godlee and Jefferson 2003; Rennie 2002). The efficacy of peer review to improve the quality of manuscripts and to minimize bias has been questioned. Some studies show benefits, while others show no benefits or negative influences from peer review (e.g., Armstrong 1997; Jefferson et al. 2002a; Jefferson et al. 2002b; Overbeke and Wager 2003). For every one of these studies, however, there are enthusiastic editorials defending the value of peer review (e.g., Gannon 2001; Tobin 2002). What seems certain at this stage is that peer review is no guarantor of the accuracy or scientific quality of a published paper (Callaham et al. 1998; Altman 2002; Horton 2002)."

There once was a time when to have a scientific paper published, it had to be - well, - scientific. Not so any more it appears. Peer Review has become more like Snob Review or Mate Review, and the so-called "prestigious" journals are making a mockery of themselves and of science.

Whilst discussing Electric Universe concepts on public forums one often comes across self-appointed xspurts* in cosmology who dismiss EU for its lack of publication in Peer-Reviewed journals. When for example, items published in the IEEE Transactions on Plasma Science are cited, then the IEEE is not considered "prestigious" enough or sufficiently qualified to comment on cosmological matters. Yet paradoxically cosmologists think themselves qualified to comment on plasma physics. They want to have their cake and eat it too. And they're not willing it seems to share the cake around.

[*x = an unknown quantity, spurt = a drip under pressure...]

Why does this matter to anyone? Because, Joe Average, not only is it your tax dollars which pay for this outrageous elitist regime, but your children are being slowly brainwashed into believing that some of the most inconceivable theories ever devised by man are now established fact. Take the so-called Big Bang for instance, which for all intents and purposes goes something like "Once upon a time, nothing went BANG!". Whilst that may seem a simplistic summary, it is none-the-less how the Fairy-Tale goes. But after years of intelligent people questioning the validity of such a concept, we now have the cosmologists answering "Oh no, it wasn't nothing which went bang, it was another universe which had contracted down to a singular point...". I kid you not. Take this recent release from that bastion of all things scientific and true, Physorg.com.Before the Big Bang: A Twin Universe?April 09, 2008 By Lisa Zyga"

You have the link. I will spare you the experience of reading the fairy tale of twin universes unless you choose to do so. But feel free...

"If Ben Stein's 2008 documentary film Expelled: No Intelligence Allowed was the tip, then Dr. Jerry Bergman's Slaughter of the Dissidents is the rest of the iceberg. With clarity and thoroughness, Bergman provides detailed accounts of 17 of the over 300 scientists and educators he has interviewed, all of whom have advanced degrees. Though their views range from creation science to intelligent design to evolution, all of them expressed some doubt regarding neo-Darwinism, observing that selection of mutations is not creating life's diversity. And all of them have received some form of discrimination.

Dr. Bergman has observed that evolutionary elitists incorrectly lump all "Darwin Doubters" into one group, "creationists," who are then categorically ridiculed. Though highly qualified, these scientists and educators are verbally and physically threatened, lose privileges, lose opportunities for promotion, and lose jobs and whole careers, just for expressing some measure of doubt about the standard evolutionary story."

" The first chapter, “A Context for Discrimination Against Darwin Skeptics” deserves special recognition. Kevin Wirth, who authored it, did an excellent job providing a background and context for this book, especially for those not familiar with the debate or why it generates so much controversy. It almost deserved to be an entire book unto itself. It described why (a) Darwin skeptics are skeptical, (b) Darwinists are skeptical of the skeptics, (c) why ID’ers and Creationists are often lumped together in a single category, even when completely inappropriate to the context, (d) the relationship between the source, the justification, and the effects of ideas (and why it matters), and (e) the relationship that religion has with this whole debate.

Honestly, if someone who wasn’t familiar with the issues asked for a short introduction to the whole issue, I would recommend that they buy the book if only to read the first chapter. That would give a good background on what the disagreement is over and why it is so heated."

A free chapter is available for download for those who go to the booksite and register.

"Is peer review broken?

1/2/06: Is peer review broken? Article by Alison McCook in The Scientist, (20)(2),26 says that submissions are up, reviewers are overtaxed, and authors are lodging complaint after complaint about the process at top-tier journals. Cites Peter Lawrence, who has been publishing papers in academic journals for 40 years. His first 70 or so papers were "never rejected," he says, but that's all changed. Now, he has significantly more trouble getting articles into the first journal he submits them to.

Lawrence, based at the MRC Laboratory of Molecular Biology at Cambridge, UK, says his earlier papers were always published because he and his colleagues first submitted them to the journals they believed were most appropriate for the work. Now, because of the intense pressure to get into a handful of top journals, instead of sending less-than-ground-breaking work to second- or third-tier journals, more scientists are first sending their work to elite publications, where they often clearly don't belong. Lately, academia seems to place a higher value on the quality of the journals that accept researchers' data, rather than the quality of the data itself. In many countries, scientists are judged by how many papers they have published in top-tier journals; the more publications they rack up, the more funding they receive.

The recent discrediting of stem cell work by Woo-Suk Hwang at Seoul National University sparked media debates about the system's failure to detect fraud. Authors, meanwhile, are lodging a range of complaints: Reviewers sabotage papers that compete with their own, strong papers are sent to sister journals to boost their profiles, and editors at commercial journals are too young and invariably make mistakes about which papers to reject or accept.

The article says that, despite a lack of evidence that peer review works, most scientists appear to believe in peer review. Indeed, an abundance of data from a range of journals suggests peer review does little to improve papers. In one 1998 experiment designed to test what peer review uncovers, researchers intentionally introduced eight errors into a research paper. More than 200 reviewers identified an average of only two errors. That same year, a paper in the Annals of Emergency Medicine showed that reviewers couldn't spot two-thirds of the major errors in a fake manuscript. In July 2005, an article in JAMA showed that among recent clinical research articles published in major journals, 16% of the reports showing an intervention was effective were contradicted by later findings, suggesting reviewers may have missed major flaws.

Some critics argue that peer review is inherently biased, because reviewers favour studies with statistically significant results. Research also suggests that statistical results published in many top journals aren't even correct, again highlighting what reviewers often miss. Moreover, peer review can also err in the other direction, passing on promising work: Some of the most highly cited papers were rejected by the first journals to see them. There is also a suggestion that reviewers were less likely to reject a paper if it cited their work, although the trend was not statistically significant.

"Richard E Smalley, winner of the 1996 Nobel Prize in chemistry, as asked to present the keynote address at Tuskegee University's 79th Annual Scholarship Convocation/Parents' Recognition Program. In his address he discussed the increasing lifespan of humans as a result of cures and treatments for various infections and diseases. He urged his listeners to seriously consider their role as "higher species" on this planet. He also mentioned the ideas of evolution versus creation, Darwin versus the Biblical Genesis account, noting that the burden of proof is on those who do not believe that "Genesis was right, and there was a creation, and that the Creator is still involved". (1)

After reading the book "Origins of Life" by Fazale Rana and Hugh Ross (2), among other books by Rana, Richard Smalley make the following endorsement: " Evolution has just been dealt its death blow. After reading Origins of Life, with my background in chemistry and physics, it is clear evolution could not have occurred." (3)

Toward the last days of his life, in an interview with William Dembski, Smalley predicted that ID would be mainstreamed in five years and that evolution, in its conventional materialistic sense, would be dead within ten. Although I am personally just a bit skeptical as to the time frame, it will be interesting to see if his predictions are eventually borne out. (4)

Five years? Nah, Pasteur disproved spontaneous generation in 1861 and yet pure Darwinists must believe it in order for their beliefs to make any sense. Hey, if God was capable of starting life then wouldn't He be capable of giving us a Bible to tell us about it? He wouldn't need gagagazillions of mutations and years to bring the world to its present state. I am thinking maybe at least ten more years and more likely twenty. I mean, isn't continuing to re-try some form of Miller-Urey experiment over and over again something like the definition of insanity? Har.

Darwinism is an alibi that is being exposed as fraudulent. Before naturalistic materialistic scientists can give it up, they need to think up another one. Something other than God, because the anything-but-God motive has driven Darwinism for several decades now.

I am willing to give Darwinists the benefit of the doubt before the intricate nature of the cell became apparent and before we discovered the amazing wonder of DNA. But now that we understand the obvious design features of life they are now without excuse. I don't write this to convince those desperate to hang on to failed and laughable science, no matter how orthodox and widely taught. I say this to those who still have open minds. Look into this carefully for yourselves...don't take the pat answers at face value.

Peer review amongst the orthodox crowd is a failed and prejudicial system. Like the old Jim Crow laws, unbelievers are forced to use their own figurative fountains and motels and restaurants because the "No Creationists or ID'ers" have been hung up over the ones frequented
by the "superior" Darwinist crowd. Mockery. Derision. Segregation. A scientific apartheid exists in that good scientists who are of the wrong point of view are forced to seek to be "separate but equal." It is to the shame of the majority of the scientific community that dissension is stifled and careers ruined and it is also contrary to the advance of scientific knowledge.

32 comments:

Yo... Gonzalez never lost tenure... he never had it in the first place (I'm sure you've been corrected on this in the past as well). This thing you do where you constantly repeat things you've been shown to be wrong on in the past is getting incredibly old. Come over to the dark side already... it'll be much better than this constant cognitive dissonance you must be experiencing.

IAMB, are you saying he should just shrug off the cognitive dissonance and accept science or just start lying full time?

You beat me to the punch about Gonzalez. Even the hilarious conservapedia site says he never had tenure, though in three sentences they say that he was one of three professors denied tenure, and that his department denies 1/3 of its professors tenure.

Why is it not a double standard to reject peer reviewed papers by Creationists who are peer reviewed by Creationists and than accept peer reviews by evolutionists? At what basis does the average Joe like myself finally come to a conclusion? I find it hard to swallow that something is "established fact" because a group of like-minded individuals decide that a theory is/isn't plausible.

"Creationists who are peer reviewed by Creationists and than accept peer reviews by evolutionists?"

Because that's not what's happening. According to IAMB, Creationists aren't even bothering to submit their papers for peer review, and are instead moving on to claiming discrimination. Court records have shown this to be the case.

"At what basis does the average Joe like myself finally come to a conclusion? "

First, you have to care. ;)Then realize that proposing a theory that explains life better than evolution will pretty much be the pinnacle of your *life* if you're a scientist. It's not like scientists are swearing fealty to orthodoxy here. They use evolution to do actual work (like IAMB does) every day. It explains and makes sense of the data they see. If it didn't work, they'd quickly replace it with something that does. That's why so many scientists vociferously oppose creationism, they see it as a threat to future progress.

When I'm at work, if something isn't helping me do my job, I replace it with something that does. I might have a hypothesis of why the web site is breaking, but if the my hypothesis doesn't fit the data, do I cling to it? Hardly --my hypothesis is thrown out for another one.

I know for a fact that science works the same way.

Also, and this will be tough, ask yourself: If you weren't a Christian, would you believe in the Christian cosmology? Keep in mind that this requires that you don't view the Bible as factual at all, you would view it just like you currently views the Bhagavhad Gita --as a literary work.

Tim, it would be a double standard if information in creationist "peer-reviewed" papers could be verified instead of easily be shown false. For instance, the article Radar quotes here from the Answers journal again makes the claim that creationists are excluded from publishing in mainstream journals... yet public record shows that they've never - again: never - tried. If I submit something and it's rejected, there's a letter of rejection and it's part of the record. If creationists had papers on creationist subjects rejected, they would be easy to produce in court whenever the exclusion argument came up. Why do you think that's never happened?

The blatant dishonesty is why I reject claims made in creationist journals.

They have no respect for the integrity or intelligence of the people who subscribe to their beliefs, else they'd try hiding their lies a little more carefully. Why would you ever trust people like that?

You conveniently mentioned Answers Research Journal. Let's have a look at ARJ's Instructions to Authors:VIII. Paper Review ProcessUpon the reception of a paper the editor-in-chief will follow the procedures below:A. Receive and acknowledge to the author the paper’s receipt.B. Review the paper for possible inclusion into the ARJ review process.The following criteria will be used in judging papers:1. Is the paper’s topic important to the development of the Creation and Flood model?2. Does the paper’s topic provide an original contribution to the Creation and Flood model?3. Is this paper formulated within a young-earth, young-universe framework?4. If the paper discusses claimed evidence for an old earth and/or universe, does this paper offer a veryconstructively positive criticism and provide a possible young-earth, young-universe alternative?5. If the paper is polemical in nature, does it deal with a topic rarely discussed within the originsdebate?6. Does this paper provide evidence of faithfulness to the grammatical-historical/normative interpretationof Scripture? If necessary, refer to: R. E. Walsh, 1986. Biblical hermeneutics and creation. ProceedingsFirst International Conference on Creationism, vol. 1, pp. 121–127. Pittsburgh, Pennsylvania: CreationScience Fellowship.

It can't get any clearer than that: only papers that support creationism, the flood model and scripture will be accepted. Radar, it appears that your own creationist buddies from ARJ are guilty of exactly that which you are accusing those 'evil evolutionist scientists' of. This is clear proof. Now, Radar, I'm gonna ask you exactly the same thing I asked you back then:

Please point us to author instructions from reputable scientific magazines that clearly state that articles that support a global flood, creationism, or biblical scripture are NOT accepted, or otherwise unambiguously display censorship or hostility towards those ideas.

I dare you, Radar!

And then there's this statement:

First of all, from Answers Research Journal (ironically, a peer-reviewed publication).

Are you willing to be consistent and state that ARJ, and by extension Answers in Genesis which sponsors it, is "farcical, and a members-only club that excludes ideas not considered sci-politically correct."?

First, Gonzalez was DENIED tenure. You are parsing words. He was over-qualified for tenure, if anything. His tenure was denied after a nasty email campaign set up against him by humanist zealots and an anti-ID website set up in response to his work. He was denied tenure, and twice denied appeal of tenure.

http://www.wnd.com/index.php?fa=PAGE.view&pageId=55826

"Officials with Evolution News, which has reported extensively on the case, earlier said two of the professors linked to the statement were in the astronomy and physics department: Prof. Steven Kawaler, who has linked to the statement on his website, and University Professor Lee Anne Willson, who is married to ISU math professor Stephen J. Wilson, who signed it.

Evolution News also debunked Rosenberg's claim that there was something deficient about Gonzalez's research record.

"You take a look at somebody's research record over the six-year probationary period and you get a sense whether this is a strong case. Clearly, this was a case that looked like it might be in trouble," Rosenberg had said.

"Really?" questioned Evolution News in its commentary. "Was Gonzalez somehow derelict in publishing 350 percent more peer-reviewed publications than his own department's stated standard for research excellence? Or in co-authoring a college astronomy textbook with Cambridge University Press? Or in having his research recognized by Science, Nature, Scientific American and other top science publications?"

In 2004 Gonzalez department nominated him for an "Early Achievement in Research" honor, his supporters noted.

According to Robert J. Marks, distinguished professor of electrical and computer engineering at Baylor, he checked a citation index of journal papers, and found one of Gonzalez' research papers had 153 citations listed; another had 139.

"I have sat on oodles of tenure committees at both a large private university and a state research university, chaired the university tenure committee, and have seen more tenure cases than the Pope has Cardinals," he said. "This is a LOT of citations for an assistant professor up for tenure."

I dare anyone to read that entire article and deny that Gonzalez' career was sabotaged on religious grounds, that is, that he was not a naturalistic materialist and thereby censured.

~

Second, I was generalizing about the climate in the scientific community concerning peer review. Gonzalez, for example:

"Dr. Gonzalez has an impressive list of achievements including:

* 68 peer-reviewed scientific articles; * a college-level astronomy textbook published by Cambridge University Press; * spearheading research that led to the discovery of 2 new planets; * being asked to serve as a referee for a number of leading scientific publications.

Dr. Gonzalez’s research has been featured in Science, Nature, and on the cover of Scientific American.

“Given his outstanding record, it’s clearly preposterous to claim that Dr. Gonzalez is somehow deficient as a scientist. If anything, the problem is likely that he is too good. Darwinist professors can’t stand the thought of allowing a gifted scientist who supports intelligent design into their ranks. This is despite the fact that Gonzalez’s work focuses on design in cosmology, and does not even address biological evolution.”

ID/Creationists include hundreds of highly respected men who had plenty of papers accepted for peer review until they revealed their worldviews, at which point their papers would usually be rejected.

Dr. Sarfati is a very personable man who I was fortunate to meet a couple of years ago and we conversed, in part, on this very subject. He seemed unconcerned by the peer review problem because the organization he was involved with (CMI) had a system of peer reviewed and refereed publications in place. I subscribed to them and have found them a wonderful source of information, although the newer resources are not available on the web.

The point is that creationist and ID scientists are now tending to quit wasting time trying to get peer reviews elsewhere and turning to journals and publications that do not discriminate against them and allow them to post on the merit of their evidences.

~Plenty of creationists and ID scientists have published thousands of peer-reviewed papers, won various prizes and honors, etc. But colleagues turn away from them when they reveal a different point of view.

IAMB, you would have to be omniscient to back up your statement - "yet public record shows that they've never - again: never - tried." That is a lie, don't believe it. You cannot possibly prove it.

I have just proved that they have, indeed, gotten published in peer reviewed journals regularly up until they reveal their world views. Your statement is amazing and hopefully no one could take such a claim seriously. Please rethink what you have written. As I said, you would have to be omniscient to know and prove that no such scientists have EVER had their work rejected.

~~~~~~

Third, that that T Rex was bone and not fossil was beyond question in the eyes of scientists at one time. Sweitzer herself had the finding of dinosaur soft tissue and probably blood cells trumpeted all over the world, via Nova and Smithsonian magazine and many other mainstream media and science journal sources and then she and Horner and others backed off the claims when the implications hit them...if these were blood cells, then the whole "long ages" hypothesis is looking very bad.

The Darwinist side has published several retractions, saying that blood was actually something else. While there is evidence to suggest the remains of blood cells are present, it does not benefit the Darwinist side to admit to that.

~~~~~~~

Once there were tracks that appeared to be human along the Paluxy riverbed that were destroyed by someone and others that were sold off by opportunists before WWII. I followed up on the hypothesis that a particular Darwinist scientist may have done the dirty deed but further research made that unlikely. We will probably never know. The point being, if any evidences that support a young earth or creation are discovered, naturalistic materialistic scientists close ranks and deny and, perhaps, even hide or destroy that evidence or those findings.

Some secular peer-reviewed journals are reviewing their policies and we may soon see some creationist articles being accepted in mainstream publications. But for an illustration of how things really are right now, catch my next post. Because of the efforts of organizations such as CMI, the worm may be turning in the near future.

According to IAMB, Creationists aren't even bothering to submit their papers for peer review, and are instead moving on to claiming discrimination.

More even: they admit it themselves. Here's Michael Behe at the Dover Trial:

On cross-examination, Professor Behe admitted that: “There are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred.” (22:22-23 (Behe)). Additionally, Professor Behe conceded that there are no peer-reviewed papers supporting his claims that complex molecular systems, like the bacterial flagellum, the blood-clotting cascade, and the immune system, were intelligently designed. (21:61-62 (complex molecular systems), 23:4-5 (immune system), and 22:124-25 (blood-clotting cascade) (Behe)). In that regard, there are no peer-reviewed articles supporting Professor Behe’s argument that certain complex molecular structures are “irreducibly complex.”17 (21:62, 22:124-25 (Behe)). In addition to failing to produce papers in peer-reviewed journals, ID also features no scientific research or testing.

There you have it, straight from the horse's mouth. It's not only that there are no papers, there's even no scientific research that supports Intelligent Design (which really IS your daddy's creationism). No wonder of course, since the 'cdesign propenentists' rather spend their donations on propaganda movies or creation museums.

Yes, ARJ is a journal with a point of view, a place of refuge for scientists who hold that point of view.

Some history -

Major League Baseball did not have a rule that stated Black players were not allowed. Yet, from the late 1800's onward no Black baseball players were allowed to play major league baseball or their top affiliated minor league clubs. Was there writing in place that stated the rule? No, it was unwritten. Yet it was ironclad until Branch Rickey decided to heroically defy the baseball establishment and sign great ballplayers such as Jackie Robinson and Roy Campanella and, in 1946 the minor league barrier and in 1947 the major league baseball color barrier was broken.

Did Robinson and Campanella just stand around on street corners waiting for a Branch Rickey to show up? No, the barred "colored" players formed their own leagues and played seasons with great stars such as Josh Gibson and Satchel Paige, men every bit as talented as Joe Dimaggio or Bob Feller.

The Mexican League also welcomed star Black players when MLB was loathe to do so. Campy began his career there, but moved to Nashua in 1946, a Dodger farm team, where he and Don Newcombe became the first B league "colored" players. Jackie Robinson joined "A" league Montreal that same year. Robinson had been playing with the Negro League Kansas City Monarchs, while Newk had been with the Newark Eagles.

Robinson and Campanella and Newcombe would have had long and successful careers in the Mexican or Negro Leagues had Rickey not had the guts to open MLB up to players of color. But the general public would have had little chance to see their talent and the major leagues would have been lessened by their absence.

Now we have players of all races and from many foreign countries playing MLB and NFL and NBA ball.

The ARJ and JOC are the equivalent of the Negro Leagues of the whites-only era of major league baseball. Brilliant scientists will research and publish. If they cannot publish in Nature magazine, they will do it in ARJ or the Journal of Creation, etc.

"The part of Kitzmiller that finds ID not to be science is unnecessary, unconvincing, not particularly suited to the judicial role, and even perhaps dangerous both to science and to freedom of religion”

--Jay D. Wexler, Anti-ID legal scholar at Professor of Law, Boston University Law School

Behe was asked leading and twisted questions, then his answers were again twisted. The trial was a joke. Jesus was convicted by the Sanhedrin, that doesn't mean He was guilty. Combine false witnesses and a judge predisposed to convict and, voila!

[Editor's note: This article was posted as part of a series of articles both for and against ID at OpposingViews.com.]

"The part of Kitzmiller that finds ID not to be science is unnecessary, unconvincing, not particularly suited to the judicial role, and even perhaps dangerous both to science and to freedom of religion”1--Jay D. Wexler, Anti-ID legal scholar at Professor of Law, Boston University Law School

ID has legal and educational merit because it is a bona fide scientific theory that can enhance the effectiveness of science instruction.

A Preliminary PointBefore explaining the legal and educational merit of teaching intelligent design (ID), the following point must be made clear: While I strongly believe that ID should be considered constitutional to present as a scientific alternative to evolution, I do not support mandating ID into public school curricula.

As Discovery Institute states on its education policy page, “As a matter of public policy, Discovery Institute opposes any effort require the teaching of intelligent design by school districts or state boards of education. Attempts to mandate teaching about intelligent design only politicize the theory and will hinder fair and open discussion of the merits of the theory among scholars and within the scientific community.

Furthermore, most teachers at the present time do not know enough about intelligent design to teach about it accurately and objectively.”

In the wake of the Kitzmiller v. Dover lawsuit, there has been an intense spike in the persecution of teachers, students, and faculty who support ID. The ID movement’s priority is to see ID advance through scientific research, and in today’s hostile political climate, school districts that require ID do more to harm ID than to help it. The long-term success of ID depends on its scientists having opportunities to produce good scientific research and scholarship, and not being constantly dragged before courtrooms or school boards to defend ill-conceived educational policies.

Thus, in arguing that ID has legal and educational merit, I am not therefore arguing that the best thing for the scientific progress of ID is to force it into public schools. Far from it. Nonetheless, I do think that ID should be considered perfectly constitutional and that teaching students about the scientific debate between ID and evolution can have great educational benefits.

Has ID Been Banned from Public Schools by the Courts?No, ID has not been banned from U.S. public schools by the courts. Contrary to popular belief, the U.S. Supreme Court has never addressed the teaching of intelligent design. In fact, the only case which has ever squarely addressed the teaching of intelligent design was a federal trial court in the middle district of Pennsylvania--a ruling that applies only to the parties in that case and does not apply to the rest of the country. (This 2005 Kitzmiller v. Dover case will be discussed extensively below.)

The arguments for the constitutionality of teaching ID are remarkably simple--on the surface. In the 1987 case Edwards v. Aguillard, the Supreme Court sanctioned the teaching of scientific alternatives to evolution provided that they were taught under legitimate secular purposes:

"[T]eaching a variety of scientific theories about the origins of humankind to schoolchildren might be validly done with the clear secular intent of enhancing the effectiveness of science instruction."

However, Edwards also struck down the teaching of creationism because creationism was a religious belief because it referred to a “supernatural creator.”

The question of whether it is constitutional to teach ID in public school science classrooms thus turns on whether ID is a scientific viewpoint, or whether it refers to a “supernatural creator” and is thereby a religious viewpoint under the Edwards ruling.

In my first opening statement ("Intelligent design (ID) has scientific merit because it uses the scientific method to make its claims and infers design by testing its positive predictions"), I argued that ID is a bona fide scientific theory because it makes its claims using the scientific method.

In my third opening statement ("Any larger philosophical implications of intelligent design, or any religious motives, beliefs, and affiliations of ID proponents, do not disqualify ID from having scientific merit"), I argued that the religious beliefs, motives, and affiliations of ID proponents, and any larger philosophical implications of ID, do not disqualify it from being scientific.

In the fourth opening statement ("ID Does Not Address Religious Claims About the Supernatural"), I explained how ID limits its claims to what can be learned from the empirical domain and does not make unscientific appeals to the supernatural that might violate methodological naturalism. I also argued that ID is distinct from creationism because it does not require a “supernatural creator” and instead only refers to intelligent causes.

What, then, stands in the way of considering intelligent design as a scientific theory?

Legally assessing whether ID science or religion is complicated by the fact that courts have not agreed upon a consensus definition of science or religion. Indeed, the U.S. Supreme Court has studiously--and perhaps wisely--avoided giving blanket definitions for those categories.

One of the few clear rules in this legal field is the U.S. Supreme Court’s Edwards holding that creationism is a religious viewpoint because it postulates a “supernatural creator.” Thus, it is unsurprising that one of the most convenient allegations made against ID is that it is simply repackaged version of creationism that invokes the supernatural, was designed to circumvent the U.S. Supreme Court’s ruling in the 1987 case Edwards v. Aguillard. As I argued in my fourth opening statement ("ID Does Not Address Religious Claims About the Supernatural"), these claims are based upon a twisting of ID and a re-writing of ID’s history.

In my fourth opening statement ("ID Does Not Address Religious Claims About the Supernatural"), I laid out the evidence documenting that ID does not try to address religious questions about the supernatural, and is distinct from creationism.

But is ID science? In fact, leading philosophers of science, such as Larry Laudan, have argued that, “[T]here is no demarcation line between science and nonscience, or between science and pseudo-science, which would win assent from a majority of philosophers.”

Because there is no consensus definition of science, lower courts have at times adopted controversial definitions of “science.” In a twist of fallacious logic, these courts tend to presume that if an idea fails that particular court’s favored definition of science, then that the viewpoint must therefore be religion.6 Such arguments ignore the fact that many types of claims--such as historical or philosophical claims--are not scientific but are also not religious.

In the 2005 Kitzmiller v. Dover case, Judge Jones employed this reasoning after finding that ID failed a 6-part test he adopted for defining science:

“[A] ID violates the centuries-old ground rules of science by invoking and permitting supernatural causation; [B] the argument of irreducible complexity, central to ID, employs the same flawed and illogical contrived dualism that doomed creation science in the 1980's; and [C] ID’s negative attacks on evolution have been refuted by the scientific community. As we will discuss in more detail below, it is additionally important to note that [D] ID has failed to gain acceptance in the scientific community, [E] it has not generated peer-reviewed publications, nor [F] has it been the subject of testing and research.”

After conducting his analysis, Judge Jones fallacious claimed that "since ID is not science, the conclusion is inescapable that the only real effect of the ID Policy is the advancement of religion.”

According to Judge Jones, since the Lemon test requires that the predominant purpose behind a law cannot be religious, and primary effect of the law must not advance religion (the effect “prong”), the Dover Area School District’s ID policy was unconstitutional.

Each of the six criteria Judge Jones used to claim that ID is not science was either incorrect or irrelevant to his analysis. In fact, since the Supreme Court held in Edwards that “[i]f the law was enacted for the purpose of endorsing religion, no consideration of [Lemon’s] second or third criteria is necessary,” arguably, Judge Jones' entire analysis of whether ID was science was irrelevant to his ruling once that he found that the Dover Area School Board had unconstitutional religious motives.

My opening statements have already rebutted some of Judge Jones’ six reasons why ID is not science, but I will review the arguments here:

A. ID does not require supernatural causation and the fact that it might permit it is irrelevant.

As I explained in my fourth opening statement ("ID Does Not Address Religious Claims About the Supernatural"), ID does not invoke supernatural causation, and the fact that ID permits it does not cause it to violate methodological naturalism. In fact, ID meets the requirements of predictability and reliability laid down by methodological naturalism. Judge Jones’ argument that ID is not science because it “requires supernatural creation” was predicated upon a false version of intelligent design that directly contradicted descriptions of ID given by pro-ID expert witnesses in his own courtroom.

B. The arguments for ID from irreducible complexity are not merely negative arguments against evolution and thus ID does not use a “contrived dualism.”

In my first opening statement ("Intelligent design (ID) has scientific merit because it uses the scientific method to make its claims and infers design by testing its positive predictions"), I explained that ID is not a merely negative argument against evolution but makes positive arguments. This means that ID does not employ the “flawed and illogical contrived dualism” when making its case, for irreducible complexity is both a positive argument for design, and a negative argument against evolution. As Michael Behe writes:

“[I]rreducibly complex systems such as mousetraps and flagella serve both as negative arguments against gradualistic explanations like Darwin’s and as positive arguments for design. The negative argument is that such interactive systems resist explanation by the tiny steps that a Darwinian path would be expected to take. The positive argument is that their parts appear arranged to serve a purpose, which is exactly how we detect design.”

Irreducible complexity is a positive argument for design because we understand that forward-thinking intelligent agents produce such a complex, purposeful arrangement of parts. It is a negative argument against evolution because neo-Darwinian pathways cannot produce structures where large leaps in complexity are required to maintain functionality. This is not a “contrived dualism.” It is an actual, logical dualism justified by our empirically-based understanding of the respective causal powers of ID and natural selection.

C. Judge Jones’ arguments that ID is unscientific because it has been “refuted by the scientific community” are both false and irrelevant.

University of Kentucky philosopher Bradley Monton observes that being wrong does not necessarily make an idea unscientific. Newtonian physics has been refuted and superseded by Einstein’s theory of relativity. But that does not make Newton’s laws of mechanics “unscientific,” and indeed, physics classes still invariably teach them alongside Einstein’s models in schools. Here it is Judge Jones who proposes the false dichotomy: he wrongly asserts that if a theory is not correct, it cannot be science. But something can be wrong and still be science.

Even if Judge Jones believed that ID is false, it was not his responsibility to investigate the scientific truth or falsity of ID. Judge Jones should have remembered that “the wisdom of an educational policy or its efficiency from an educational point of view is not germane to the constitutional issue of whether that policy violates the establishment clause.”

If courts really mean it when they say that “[s]tates and local school boards are generally afforded considerable discretion in operating public schools,” then what matters is that the school board sincerely believed that ID has scientific merit, not whether a federal judge is convinced of its ultimate scientific truth.

There are good reasons why the truth or falsity of ID’s scientific claims is irrelevant to a judicial determination of whether ID violates the Establishment Clause. Our form of government requires a separation of powers. During lawsuits alleging violations of the Establishment Clause in public school curricula, courts are allowed to determine if the curriculum establishes religion, but that’s it. Yet Judge Jones found that ID’s claims have allegedly “been refuted by the scientific community” as he sought to settle questions about the scientific minutiae of the debate, such as whether the flagellum might have evolved from a type three secretory system (T3SS) or whether the vertebrate immune system could have arisen in a Darwinian fashion. These are interesting and important questions, but regardless of whether you agree with Judge Jones’ answers, they are questions about good science vs. bad science in a curriculum, and are NOT question about an establishment of religion. Whether ID's claims constitute good science would be a question for the legislative branch to address; addressing such matters should not be within the domain of a court’s constitutional analysis.

Another reason why courts should not try to settle scientific debates is because courts don’t adequately address the issues and are not well-suited to settle scientific controversies. In fact, Judge Jones’ arguments about the alleged “refutation” of ID are highly debatable. Two examples will suffice.

Judge Jones claimed that plaintiffs’ expert witness Kenneth Miller explained how the bacterial flagellum could evolve from the T3SS. However, a number of biologists have concluded the phylogenetic data disbars the T3SS from being a precursor to the flagellum. In short, flagella are widely distributed among large numbers of types of bacteria, where as T3SSs are limited to a small range of bacterial taxa. This makes it difficult to argue that the flagellum evolved from the T3SS or a highly similar precursor.

When making conclusions about the flagellum, Judge Jones also ignored expert testimony by pro-ID microbiologist Scott Minnich, a flagellum expert who runs a lab at the University of Idaho studying the flagellum. Minnich explained that even if Miller’s speculative scenario turned out to be true, it would not be sufficient to prove a Darwinian explanation for the origin of the flagellum because there is still a huge “leap” in complexity from a T3SS to a flagellum. What we have here is evidence of a scientific debate between two experts--including a pro-ID expert who is a respected authority in this field. Judge Jones should not have tried to settle the scientific debate.

The unresolved challenge that the irreducible complexity of the flagellum continues to pose for Darwinian evolution is starkly summarized by William Dembski:

“At best the T[3]SS represents one possible step in the indirect Darwinian evolution of the bacterial flagellum. But that still wouldn’t constitute a solution to the evolution of the bacterial flagellum. What’s needed is a complete evolutionary path and not merely a possible oasis along the way. To claim otherwise is like saying we can travel by foot from Los Angeles to Tokyo because we’ve discovered the Hawaiian Islands. Evolutionary biology needs to do better than that.”

Dembski’s critique is apt because it recognizes that Miller wrongly characterizes irreducible complexity as focusing on the non-functionality of sub-parts. Conversely, Behe properly tests irreducible complexity by assessing the plausibility of the entire functional system to assemble in a step-wise fashion, even if sub-parts can have functions outside of the final system. The “leap” required by going from one functional sub-part to the entire functional system is indicative of the degree of irreducible complexity in a system.

Contrary to Miller’s assertions, Behe never argued that irreducible complexity mandates that sub-parts can have no function outside of the final system. In the end, Judge Jones’ conclusion that Miller refuted the irreducible complexity of the flagellum “based upon peer-reviewed studies” was plainly erroneous. Indeed, a review article published after the Kitzmiller ruling admits that “the flagellar research community has scarcely begun to consider how these systems have evolved.”

In another finding which was both wrong and irrelevant, Judge Jones ruled that “Dr. Miller presented peer-reviewed studies refuting Professor Behe’s claim that the immune system was irreducibly complex.” Moreover, Judge Jones found that Behe’s claims that the immune system was irreducibly complex were refuted by a large stack of papers dumped upon him during cross-examination:

“[O]n cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty-eight peerreviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system.”

Yet Behe never claimed that no papers or books are “about the evolution of the immune system”--indeed in Darwin’s Black Box, Behe wrote that “[t]here are other papers and books that discuss the evolution of the immune system.” On the contrary, Behe actually testified:

“These articles are excellent articles I assume. However, they do not address the question that I am posing. So it's not that they aren't good enough. It's simply that they are addressed to a different subject.”

Thus, what Behe actually requested was, “a step-by-step mutation by mutation analysis” of the evolution of the immune system, for Behe said he is “quite skeptical” that the papers in the literature dump “present detailed rigorous models for the evolution of the immune system by random mutation and natural selection.” Judge Jones misquoted Behe and twisted his views about the state of evolutionary literature on the origin of the immune system.

One of the 58 articles dumped on Behe was an authoritative article published in Nature the year before the Kitzmiller trial which conceded that there were major questions about step-by-step accounts of the evolution of the adaptive immune system. In that recent and authoritative paper, Max Cooper, one of the fathers of immunology, wrote that the evolutionary origin of one of the most important components of the higher vertebrate “adaptive immune system,” the immunoglobulin (IG) domain containing antibody, is currently “untraceable”:

"Also, and this will be tough, ask yourself: If you weren't a Christian, would you believe in the Christian cosmology?"

I have no idea what you're asking me here. What is Christian cosmology? As far as I can tell cosmology has to do with origins and its the Christian belief that God created everything. Are you asking me if I would still believe God created everything if I wasn't a Christian? I realize you're trying to make a point but its flying way over my head as usual.

Most of the regular commenters here have noticed the cyclical nature of Radar's posts: he puts up a claim, it is argued in detail, Radar is short a few answers, then drops or changes the subject and moves on to something else. Then, a while later, he either claims victory on the subject or pretends the discussion didn't take place by simply repeating the claim in another context.

For a while, I thought it was simply the intellectual dishonesty that was necessary for Radar to maintain his YEC stance in public and in the face of logical criticism of his claims that are not capable of standing up to such criticism.

But lately, another possibility has occurred to me. Is it possible that Radar is simply not capable of understanding some of the arguments presented in response to his claims? You've all seen him very quickly move to claims of a global conspiracy of tens of thousands of scientists in all kinds of different disciplines, but on the basic logical questions regarding his claims, he remains evasive and obtuse. What if he's not being purposely dishonest, but genuinely intellectually out of his depth? Sure, his posts can sound intelligent at first glance, but that is almost entirely because he pastes other people's work at great length. (Not that those posts aren't without their problems, as has also been discussed at length, but let's leave that aside for now.)

A case in point: Radar is sick of hearing about this one, but I think it's a good example because it actually lies outside of Radar's two usual big conspiracy theories ("Darwinism" and global warming) and yet is a good illustration of Radar's cognitive dissonance at work: the prison population argument.

To recap: Radar claimed that "My figures show that up to 11% of the prison population is Christian, many of whom were converted after being jailed." (see here). Of course he was called to back up this peculiar claim. Repeatedly. Finally he relented and returned to the subject in two separate posts (here and here). In the first of these links, Radar presents, accompanied by highly tortured reasoning, an attempt to demonstrate that 11% of the general population are "Christians" by Radar's highly selective definition. He presented no data regarding the prison population at all, even admitting that it could not be found, but then doubled down and stuck to his claim: that statement is true. "Up to" means "equal to or less than" and the numbers I have found and posted in "Debates, we have debates! Christians in US prisons? " do, in fact tell us that the number of Christians in jail populations is less than 11%, thus making my statement factual." (emphasis mine)

The logical problems in Radar's argument were two-fold: one is that he did not come up with a good explanation for the 11% in the first place (about which other posters have challenged him, to which he has failed to respond), and the other is that that 11% wasn't even about the prison population, but the general population... but as you can see in the bolded section above, Radar claimed that it backed up his claim of the 11% re. the prison population.

I've mostly focused on that second point, since it is such a glaring logical error that it is impossible for anyone with basic reasoning abilities to fail to see it, and anyone who makes such a basic mistake in public and does not retract it with great haste is either being extremely dishonest and doesn't care who knows it... or has a genuine problem comprehending basic logic.

The logical fallacy here is the fallacy of division: something true of a thing must also be true of all or some of its parts.

Now, I tried to explain this to Radar in as simplistic terms as possible: "If you know that 11% of people living in Timbuktu have gold teeth, what percentage of people living in one particular village in Timbuktu have gold teeth?" The answer is that it is impossible to know: it could be anywhere from 0 to 100%. I repeated this simple explanation, rephrased in various ways, in subsequent comments. Radar's sporadic response was that he had answered the question.

And when it was brought up to him most recently, directly citing the logical error, this was his response: "Then again, you might not really understand the difference between a born-again believer and someone who associates himself with a particular denomination or group. You may not be aware of the American predilection for multiple choice forms that lead to misinformation in terms of racial heritage and religion and so on. I don't know what you know, but I know that no one has done a good study on the percentage of actual born-again Christians in prison that I have found. No one has conclusively shown what percentage of inmates become born-again after having been incarcerated. I made a reasonable educated guess and I figured it was on the high side. Like it or lump it."

So... is it possible that the logical error, explained to him immediately before his response, simply does not compute? He does not get it and so doesn't know how to respond?

So when, for example, I present the argument that the theory of evolution does not necessitate the non-existence of God, and even if "God did it", it would still be by some mechanism – a mechanism that could very well be what scientists perceive as the theory of evolution, is it possible that Radar doesn't "get" the argument? It would explain why he continues to argue that the two are mutually exclusive and that we somehow "want" or "need" God not to exist so we can live an immoral lifestyle (even if we don't take advantage of that supposed option).

Or when I point out the logical consequences of squeezing 800,000 ice core layers into 6,000 years, or the absurdity of relying on data indicating an old Earth to support his stance on global warming, he simply doesn't understand the argument? Or when he attempts to refute ice core data with a story about how a lot of snow fell in one place, he hasn't actually looked at the data supporting viewpoints that oppose his own – or understood them?

Just something to keep in mind. I find the alternative in these cases – rampant dishonesty and of course cognitive dissonance – likewise disturbing, but I think the regular commenters here may have written off simple lack of comprehension as a plausible alternative.

Getting personal, are we? Won't work. I am confident that I am smart enough to understand geniuses but not smart enough to be one, practical enough to communicate with idiots but not one myself hopefully, and patient enough to respond to recycled and previously answered questions and statements.

You are the one who cannot wrap his mind around the difference between "born again Christian", which would be the model Christ called for and the disciples emulated, versus just a person who accepts the label of "Christian".

Half of Americans who call themselves "Christian" don't believe Satan exists and fully one-third are confident that Jesus sinned while on Earth, according to a new Barna Group poll.

Another 40 percent say they do not have a responsibility to share their Christian faith with others, and 25 percent "dismiss the idea that the Bible is accurate in all of the principles it teaches," the organization reports.

Pollster George Barna said the results have huge implications.

"Americans are increasingly comfortable picking and choosing what they deem to be helpful and accurate theological views and have become comfortable discarding the rest of the teachings in the Bible," he said. "

You see, calling yourself a Christian and actually meeting the Biblical definition are two radically different things. 80% of the population could call themselves Christians or could call themselves Mork from Ork and it wouldn't change the fact that no one has yet shown me a poll or study that represents the percentage of actual born-again believers in prison.

But you are deflecting scrutiny from the paucity of real evidence for macroevolution.

BTW, my back porch railing had six layers of snow with discernible lines between the layers. There may have been more but the naked eye could only see six. These accumulated over a nine day period rather than a nine year period. Ice cores are useful in many ways, but accurate dating for the age of the Earth is not one of them.

Some commenters, having failed to convince me that they are right (because I believe that they are wrong) then label me as stupid. Nice. Name calling is not a particularly classy methodology in advancing your argument unless you regularly inhabit bar stools and begin using the method after your fourth or fifth brewski.

It would be pointless to drag out test scores or GPA and so on, because my intelligence is not really the issue. Let's be clear. I understand Macroevolution. I think it is a very weak and fatally flawed attempt to explain life as we view it today.

I posted three different articles that showed the following -

1- Thousands of generations of bacteria have never developed a new system or become a new creature

2- Those few mutations that survive by percentage are usually disadvantageous (most significant mutations are fatal or crippling to the organism).

3- Mutations that give the organism a "new" ability are almost always a loss of information that take away other abilities that result in an apparent gain of, say, the ability to metastasize a substance otherwise not used. But the information loss impacts the organism negatively in other environments and situations. In addition, it has generally required researchers to artificially induce such situations friendly to the acquisition of the new ability.

4- Even if a single mutation has some benefit and even if it is able to be passed on in the gene pool, it is always one single mutation. Never are mutation pairs observed. New systems require many thousands of mutations (theoretically, since they are not observed).

Therefore long experiments with long lines of bacteria have, for all practical purposes, falsified the concept of evolution via mutation and natural selection.

More generations of bacteria have been observed than all the generations of man that have ever existed on Earth. Lamarckian believers have given up on their hypothesis. Time for Darwinists and NeoDarwinists to go back to the drawing board.

On the other hand, rapid speciation (microevolution) has been proven to take place in the wild without help from researchers. This shows us that one single kind of doglike animal emerging from the Ark could be the progenitor of dogs and wolves and coyotes and etc. One kind of cattle could give us oxen and cows and buffalo species.

Throw God out the window and use math to simply work back from today's human population and you find that mankind logically began with a family some 4,000 odd years ago. The exponential growth of humanity and the rough knowledge we have concerning population growth over the last few centuries underline this truth. We would be standing on each other's heads if we had been around for 500,000 years!

You guys need to get your act together. Try to find any actual experimental results that support macroevolution before you start teaching it as fact to the uninformed...Oh, too late! So how about retractions and rethinking?

Show us macroevolution actually happening and then just maybe we will see you with some kind of evidence. All you have now is conjecture and hypothesis and the strong belief that God can NOT be the answer.

Questioning your intelligence radar? Quit crying, that's nothing. I got guys logging on wanting my whole family run over by a drunk driver, some state my mom should have aborted me. You don't have haters here. Not even close.

1- Thousands of generations of bacteria have never developed a new system or become a new creature

Then you didn't read Lenski's work at all. That's exactly what his E. coli did: develop a new system. A human suddenly being able to make their own vitamin C isn't even analagous here... we already have the gene; it's just broken. The human equivalent of E. coli developing the ability to use citrate is along the same scale as a human suddenly being able to perform photosynthesis... we don't have the parts in our genome to have that capability and they must come from scratch essentially.

You also said:

4- Even if a single mutation has some benefit and even if it is able to be passed on in the gene pool, it is always one single mutation. Never are mutation pairs observed.

Wrong. Wrong. Wrong. The citrate utilization in Lenski's E. coli required at least three separate mutations. Why do you insist on ignoring this?

How about Gonzalez? If you don't already know, each university department has its own tenure requirements (my department has a certain minimum publication volume and you must also generate almost half of your own salary through grant money, plus student evaluations play a role, among other things), and your publication record prior to employment in a tenure-track job at the university is not part of the consideration. Gonzalez had a stellar record and showed incredible promise prior to employment at ISU... then his work output and grant money dropped to almost nothing. He probably would have been denied anywhere, pro-ID views or not. It also doesn't help his case that his grads never finished their doctorates while he was there, since grad students supervised is also part of the consideration.

As for my statements, why don't you look up the court records where creationists have claimed to be unfairly excluded. They've been called out on it plenty of times, and always fail to produce anything to back up the claim.

Not to mention, some creationists still do get published in mainstream journals when they submit papers on subjects covered by said journals. Why don't you ask Sarfati sometime to show copies of papers he's submitted to mainstream journals and had rejected since he started working as a creationist in 96? I bet you'll get a load of silence.

True, I'm not omniscient, but there have been plenty of chances to show where work was unfairly excluded... all it would take was a few rejection letters and I'd stand corrected. What are you waiting for?

Third, that that T Rex was bone and not fossil was beyond question in the eyes of scientists at one time. Sweitzer herself had the finding of dinosaur soft tissue and probably blood cells trumpeted all over the world, via Nova and Smithsonian magazine and many other mainstream media and science journal sources and then she and Horner and others backed off the claims when the implications hit them...if these were blood cells, then the whole "long ages" hypothesis is looking very bad.

The Darwinist side has published several retractions, saying that blood was actually something else. While there is evidence to suggest the remains of blood cells are present, it does not benefit the Darwinist side to admit to that.

Stop. Lying. You have the damn papers still (I hope). You forget the part where the bone matrix was very densely fossilized and had to sit in an EDTA bath for a week prior to extracting the blood cells?

"Now the popularist treatments of this research (e.g. in New Scientist) give the impression that the E. coli developed the ability to metabolize citrate, whereas it supposedly could not do so before. However, this is clearly not the case, because the citric acid, tricarboxcylic acid (TCA), or Krebs, cycle (all names for the same thing) generates and utilizes citrate in its normal oxidative metabolism of glucose and other carbohydrates.5

Furthermore, E. coli is normally capable of utilizing citrate as an energy source under anaerobic conditions, with a whole suite of genes involved in its fermentation. This includes a citrate transporter gene that codes for a transporter protein embedded in the cell wall that takes citrate into the cell. This suite of genes (operon) is normally only activated under anaerobic conditions.

this would be the sort of thing that mutations are good at: destroying things

So what happened? It is not yet clear from the published information, but a likely scenario is that mutations jammed the regulation of this operon so that the bacteria produce citrate transporter regardless of the oxidative state of the bacterium’s environment (that is, it is permanently switched on). This can be likened to having a light that switches on when the sun goes down—a sensor detects the lack of light and turns the light on. A fault in the sensor could result in the light being on all the time. That is the sort of change we are talking about.

Another possibility is that an existing transporter gene, such as the one that normally takes up tartrate,3 which does not normally transport citrate, mutated such that it lost specificity and could then transport citrate into the cell. Such a loss of specificity is also an expected outcome of random mutations. A loss of specificity equals a loss of information, but evolution is supposed to account for the creation of new information; information that specifies the enzymes and cofactors in new biochemical pathways, how to make feathers and bone, nerves, or the components and assembly of complex motors such as ATP synthase, for example.

However, mutations are good at destroying things, not creating them. Sometimes destroying things can be helpful (adaptive), but that does not account for the creation of the staggering amount of information in the DNA of all living things. Behe (in The Edge of Evolution) likened the role of mutations in antibiotic resistance and pathogen resistance, for example, to trench warfare, whereby mutations destroy some of the functionality of the target or host to overcome susceptibility. It’s like putting chewing gum in a mechanical watch; it’s not the way the watch could have been created. Now the popularist treatments of this research (e.g. in New Scientist) give the impression that the E. coli developed the ability to metabolize citrate, whereas it supposedly could not do so before. However, this is clearly not the case, because the citric acid, tricarboxcylic acid (TCA), or Krebs, cycle (all names for the same thing) generates and utilizes citrate in its normal oxidative metabolism of glucose and other carbohydrates.5

Furthermore, E. coli is normally capable of utilizing citrate as an energy source under anaerobic conditions, with a whole suite of genes involved in its fermentation. This includes a citrate transporter gene that codes for a transporter protein embedded in the cell wall that takes citrate into the cell.6 This suite of genes (operon) is normally only activated under anaerobic conditions.

this would be the sort of thing that mutations are good at: destroying things

So what happened? It is not yet clear from the published information, but a likely scenario is that mutations jammed the regulation of this operon so that the bacteria produce citrate transporter regardless of the oxidative state of the bacterium’s environment (that is, it is permanently switched on). This can be likened to having a light that switches on when the sun goes down—a sensor detects the lack of light and turns the light on. A fault in the sensor could result in the light being on all the time. That is the sort of change we are talking about.

Another possibility is that an existing transporter gene, such as the one that normally takes up tartrate,3 which does not normally transport citrate, mutated such that it lost specificity and could then transport citrate into the cell. Such a loss of specificity is also an expected outcome of random mutations. A loss of specificity equals a loss of information, but evolution is supposed to account for the creation of new information; information that specifies the enzymes and cofactors in new biochemical pathways, how to make feathers and bone, nerves, or the components and assembly of complex motors such as ATP synthase, for example.

However, mutations are good at destroying things, not creating them. Sometimes destroying things can be helpful (adaptive),7 but that does not account for the creation of the staggering amount of information in the DNA of all living things. Behe (in The Edge of Evolution) likened the role of mutations in antibiotic resistance and pathogen resistance, for example, to trench warfare, whereby mutations destroy some of the functionality of the target or host to overcome susceptibility. It’s like putting chewing gum in a mechanical watch; it’s not the way the watch could have been created.

As Dr. Batten concludes: "Behe is quite right; there is nothing here that is beyond ‘the edge of evolution’, which means it has no relevance to the origin of enzymes and catalytic pathways that evolution is supposed to explain."

Oh, and they did find blood cell remains in that T Rex whether it took extraordinary means to do so or not. That part of that T Rex was remains and not fossillized is still the point.

I am not complaining because I am hurt emotionally by someone questioning my intellect. That has no particular impact on me personally.

It is a matter of people finding another way to dodge the issues. It is a boring method of ignoring evidence. People want to discuss my intellect or go back to some old and largely irrelevant side issue from months or even years ago in order to take attention away from the important points. Bo-ring!

Right now I am focusing on evolution at the bacteria level in this comment thread. I made points, IAMB countered and I countered him. That is dialogue and valid discussion.

Cognitive dissonance must be the 2009 phrase of the year. Yahoo! My Cognit is perfectly non-dissed, thanks anyway.

...and now I am healthy enough to leave this prison of mine, the house, and go to youth group. I am just going to sit there like some aged king receiving visitors (or some scruffy beggar sitting beside the building entrance. Choose the image you prefer for me). Yep, I will just be sitting around but it is part of my healing, as is going back to blogging and getting back to working.

If all goes well I can begin taking short walks next. Man I am tired of being cooped up at home or being in hospital rooms!

My promised next post will be tonight or tomorrow concerning further proof that ID and creationists are kept from presenting papers in secular journals and being presented to the public. Censorship? Absolutely. But my post will also reveal that some of those attitudes may be about to change...

Yes, ARJ is a journal with a point of view, a place of refuge for scientists who hold that point of view.

Thank you, you just proved my point. It's now blatantly obvious that you use a double standard: you accuse mainstream scientific journals of censorship while having no proof whatsoever to back that up. Yet, when it's proven without a shadow of a doubt that your creationist buddies do exactly that, you call it 'a place of refuge for scientists who hold a different view'. Here's a hint: people who apply double standards are usually not taken very seriously.;)

Basically, Behe's verbal victory worked in his own head but was a spectacular defeat in the eyes of anyone with a vaguely rational view of what appropriate standards of evidence in science might be (that is: when you propose and test hypotheses you have good science, when you demand impossible levels of proof before accepting anything you are engaging in pseudoscience). When this was coupled to Behe's nonanswers to questions like "Well, Dr. Behe, where is the detailed, testable ID explanation for the origin of the immune system?" it was all over.

By the way, Radar: it would have sufficed to just insert a link to the article. Why insist on relentless copy/pasting?

Behe was asked leading and twisted questions, then his answers were again twisted. The trial was a joke. Jesus was convicted by the Sanhedrin, that doesn't mean He was guilty. Combine false witnesses and a judge predisposed to convict and, voila!

Barack Obama is an attorney and, as an officer of the court, is pledged to uphold laws of the land. Yet he allowed his aunt, here in this country illegally, to live in Boston in public housing and did nothing. He didn't help support her, he didn't try to help her get a visa and, since she lost her first bid at staying legally, didn't notify authorities to have her deported. That is a violation of the law as an attorney.

Comments regarding this were strewn through your posts of the month of November until the 17th. Basically, you concluded on that day: I thought we settled that according to the language of the law he may have broken the law if you accept some assumptions that seem likely.

You never stated the assumptions you made, cited the laws you think he broke (lobo cited a couple, which required action by Obama not inaction as he was accused of initially), and especially how he supposedly violated the law as an officer of the court.

I didn't keep stringing this along...because...well, you tired me out. You didn't convince me. You buried the discussion, failed to concede that you misunderstood something, and clung to some ridiculous belief without ever providing any logical and factual backup.

No more than the usual - just considering an alternative explanation for your evasion of a number of arguments, and this explanation seems to fit in with your posts and comments. Barring rampant dishonesty, the possibility that you simply fail to comprehend a number of arguments and some very basic logic is a highly plausible one at this point - confirmed again by your response to my comment.

"Won't work."

Evidently. Drawing your attention to the fact that you're obtuse to certain arguments and one argument in particular has so far only led to you... continuing to be obtuse about it.

Which confirms to me that somehow you just don't "get" the argument, even though it is presented to you in extremely simple terms.

"I am confident that I am smart enough to understand geniuses but not smart enough to be one,"

Speak for yourself, but I'm not confident that either you or I are smart enough to understand geniuses. And given the basic lack of elementary reasoning that you display on your blog, I'll have to write this off as massive hubris on your part.

"practical enough to communicate with idiots but not one myself hopefully, and patient enough to respond to recycled and previously answered questions and statements."

If you're trying to imply that you did previously respond to the questions and statements re. the prison population:

(1) Then it should be extremely easy for you to respond to Lava's challenge to present your explanation. IIRC he's reminded you of this more than once.

(2) Please show where you ever responded to the central part of my criticism of your "logic", namely that it is a fundamental error, a fallacy of division. You have always responded to this with the same brush-off as you do here. If you think you have responded to it, just put up a link to where you think you did that and prove me wrong.

To make this plain as day one more time: my central criticism of your claim is not the highly questionable reasoning (which you still haven't shown to Lava, by the way) that you used to arrive at the 11%, and so it is completely irrelevant to respond by how I don't understand born-again Christians etc. It doesn't matter how well or how little I understand born-again Christians, as that has no bearing on the logical fallacy in question.

Again:

"Having data that show that something applies to x% of a group does not allow you to conclude that the same thing applies to x% of an arbitrary subset of that group. For example, if you know that 10% of the population of Timbuktu wear fake moustaches, you can simply not conclude from that that 10% of a village somewhere in Timbuktu wear fake moustaches. It is possible that anywhere from zero to 100% of the inhabitants of that village wear fake moustaches."

Do you get that?

Continue to evade, and the answer is obvious: you don't understand the argument in the first place. (Or you're being rampantly dishonest, but I don't want to impugn your motives.)

"But you are deflecting scrutiny from the paucity of real evidence for macroevolution."

Not at all, I'm happy to discuss those as well, and have spent a lot of time doing so, including drawing scrutiny to your flawed arguments on that topic. We can (and will) return to a lot of the open questions from that subject, don't worry.

But like I said, I find this an interesting example because it shows such extreme errors in reasoning in an area that lies outside your usual conspiracy theory areas ("Darwinism" and global warming).

"BTW, my back porch railing had six layers of snow with discernible lines between the layers. There may have been more but the naked eye could only see six. These accumulated over a nine day period rather than a nine year period. Ice cores are useful in many ways, but accurate dating for the age of the Earth is not one of them."

And is your back porch used for ice core layer sampling?

See, that's what I mean: to think that talking about the snow in your backyard has in all seriousness got anything to do with ice core layers betrays a basic lack of understanding of that subject. (And that's leaving aside for now that data from ice core layers are crucial to one of your two hobby horses, namely global warming/cooling - simply going by the written record alone is nowhere near enough to reach any meangingful conclusions to the level of detail required in climate science - and yet here you are claiming that they are completely unreliable because of the snow in your backyard.

Cognitive dissonance, sure, but there's also an overwhelming ignorance of the subject at hand that can not be denied.

That's another thing that really bothers me about the anti-science types. They look at a trivial observation and think they've discovered something that no one has ever thought about before. They imagine themselves going up to a polar researcher and saying "my back porch railing had six layers of snow" and then the researcher slaps herself on the forehead and exclaims "Oh no! All of the assumptions I've made have been totally wrong. Thank you for bringing this important and overlooked data to my attention, Mr. Valiant backyard researcher". When you think of it, this line of reasoning is incredibly insulting to people who have bothered to learn about a subject.

Radar, sorry to pile on, but please recall the statement you made a *long* time ago (March '06) that the ACLU gets "a large part" of their funding from the "tax dollars". This highlights a similar error: moving goalposts. When confronted with an error, you often say something along the lines of "well, x can be construed as y, and y is correct, so I win". In the prison population example, you said that "up to" 11% of the population could be Christian, meaning anywhere in the range of 0-11%. Such statements are meaningless on their face; I could claim that up to 100% of all rapists are dogs, meaning anywhere in the range of 0-100%. Still, there's a lot of 'splainin' to be done around the prison population.

You know what's funny? When I wrote the post on my blog discussing the ACLU issue, I came to the same conclusion that Creeper did. I also said I'd give up talking to you... but I just can't quit you! I look back at the blog post, and actually think it's quite mean-spirited. Personally, I don't think you're dumb, but we do have a fairly large issue before us.

What really sticks in my craw is that if you can't find *any* numbers about how many Real True Christians ® are incarcerated, why not just say you don't know? Why stick by this bogus 11% number? It does nothing but hurt your credibility.

"What really sticks in my craw is that if you can't find *any* numbers about how many Real True Christians ® are incarcerated, why not just say you don't know? Why stick by this bogus 11% number? It does nothing but hurt your credibility."

I will try not to be sarcastic, but I have said several times that there IS NO STUDY DONE AND NO ONE KNOWS!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!I would be included in the set "no one", wouldn't I? I explained more than once that I played with what data I could find to come up with thumbnail estimate that I thought was probably way larger than the actual percentage and I did so because there are no surveys that have specified born-again Christians in the prison population and how many of them might have been born-again before entering said population.

I do not how how much simpler I can make this for you guys. This is an example of the boring attempts to deflect the topic from uncomfortable information.

Then realize that proposing a theory that explains life better than evolution will pretty much be the pinnacle of your *life* if you're a scientist. It's not like scientists are swearing fealty to orthodoxy here. They use evolution to do actual work (like IAMB does) every day. It explains and makes sense of the data they see. If it didn't work, they'd quickly replace it with something that does. That's why so many scientists vociferously oppose creationism, they see it as a threat to future progress.

I would be fascinated to know how Darwinist theory has anything to do with IAMB's actual work. At what point does he label a petri dish "evolving" and come back a few years later to see if anything happened? I am sure he uses good operative science that is not directly related to evolution at all. I am all ears, enlighten me!

See, that's what I mean: to think that talking about the snow in your backyard has in all seriousness got anything to do with ice core layers betrays a basic lack of understanding of that subject. (And that's leaving aside for now that data from ice core layers are crucial to one of your two hobby horses, namely global warming/cooling - simply going by the written record alone is nowhere near enough to reach any meangingful conclusions to the level of detail required in climate science - and yet here you are claiming that they are completely unreliable because of the snow in your backyard.

Blah blah blah. Study of ice cores shows that many, perhaps hundreds of layers can be formed in one year. Markers associated with volcanic activity are the best way to try to date layers, but we only have good historical data for volcanic eruptions in recent history. Take us back past Vesuvius or around there and we are no longer in possession of markers that we can validate.

We have also learned that various substances migrate through levels, that levels combine in many cases, and that we really have no idea what the ice age ecology means for ice layering. Put it all together and ice cores are not good for going back and getting reliable data more than maybe three thousand years or so.

We entered a global cooling period in 1998. I warned everyone this summer that we were in fact entering a global cooling phase and, guess what, this winter has been pretty darned cold and snowy, hasn't it? Global cooling and warming are fueled by solar activity or the lack thereof. If we are entering a Maunder period then bad winters will keep on coming. Carbon dioxide levels respond to warming and cooling, but as a result rather than a cause, they are part of a complex system involving cloud and snow covers, ocean currents, etc. This system reacts to cooling conditions by bringing about system adjustments that help warm the planet and vice versa. But it is the Sun that is in charge of it all, the global systems that help balance things out are subject to Solar energy first and foremost.

You all now know more than Al Gore will admit to knowing about global warming and cooling. Then again, he stands to make millions from cap and trade policies and I don't, so telling the truth doesn't keep me from affording rides on private jets.

creeper: "[...] And that's leaving aside for now that data from ice core layers are crucial to one of your two hobby horses, namely global warming/cooling - simply going by the written record alone is nowhere near enough to reach any meangingful conclusions to the level of detail required in climate science [...]"

Radar: "Blah blah blah"

Since you fit into the subset of YEC believers / global warming skeptics: is there a YEC-compatible kind of climate science? You appear incapable of seeing the contradiction, which is most glaringly presented here:

creeper: "it's always amusing when you take a foray into the global warming/cooling debate, since it is so completely at odds with your YEC beliefs. How you manage to maintain both these positions (YEC and just about any position on global warming/cooling that is supposedly based on science) in your head at the same time is truly baffling. The problem is this: All climate research*, whether it argues for or against global warming, is based on data that presumes an old Earth, i.e. one that is more than 6,000 years old. All these quotes that you so adoringly cut-and-pasted above... are all based on research using methods that you, Radar, think are completely wrong. Your position on the global warming and cooling should not be on either side, but a huge protest that it's all based on nonsense, i.e. the presumption that the world is far more than 6,000 years old."

Radar: "Ad nauseum argument. You are simply wrong. Climate research includes records that have been strictly kept for many years, recorded by man. There are also accounts and records within the historical timeframe of mankind in which conditions and observations tell us the basics of what climates were like at different times in mankind's history. Evidences from the last few thousand years based on human observation and documentation yield all the information I need and depend on to make conclusions about how the climate works." (emphasis mine)

This is followed by (and with no apparent sense of irony) a cartoon that features data from the ISPCC, which is of course based on all those sources that Radar claims aren't necessary.

But if YEC types actually took their own claims (and the consequences thereof) seriously, why don't they come up with a kind of climate science based on the sources they would deem legitimate and leave out the ones they don't?

Granted, that wouldn't get them much, since the written record of actual temperatures only goes back approx. 200 years, and before that there are some mentions of Greenland being warmer at some point (so I guess you put "warmer" in that part of the graph) and the like...

Radar's probably sick of hearing this term, but it is the very definition of "cognitive dissonance" to accept a source of data to back up one's position in one context and claim that very same source of data is part of a global "bad science" conspiracy in another context.

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The best thing to give to your enemy is forgiveness; to an opponent, tolerance; to a friend, your heart; to your child, a good example; to a father, deference; to your mother, conduct that will make her proud of you; to yourself, respect; to all men, charity.Francis Maitland Balfour